INTRODUCTION============PePr is a ChIP-Seq Peak-calling and Prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution. PePr empirically estimates the optimal shift/fragment size and sliding window width, and estimates dispersion from the local genomicarea. Regions with less variability across replicates are ranked morefavorably than regions with greater variability. Optional post-processing steps are also made available to filter out peaksnot exhibiting the expected shift size and/or to narrow the width of peaks.

INSTALL=======if you want to use pip to install PePr(recommended): if pip package is intalled in your system: simply run `pip install PePr` else: install pip and then run `pip intall PePr`else if you don't want to use pip (going the harder way): manually download and install the dependencies if not already installed(numpy, scipy and pysam); download PePr and unzip (tar zxvf PePr-version.tar.gz); go into the PePr directory and type `python setup.py install`.

You can test the intallation by running the example code in the PePr/data directory to see if it gives the same results as provided.